library(here)
## here() starts at D:/git/atlantic-series/ATLANTIC_CAMTRAP
library(ggplot2)
library(forcats)
library(RColorBrewer)
Gráficos para o datapaper Atlantic-Camtraps. Adaptado e organizado a partir da primeira versão criada por Renata Muylaert.
pH Fernando Lima, D.Sc.
RM Renata Muylaert, D.Sc.
MR Milton Ribeiro, D.Sc.
ADICAO DE COMENTARIOS: Corpo do Texto: insira suas iniciais entre
** e depois os comentarios: e.g. **pH**
blablabla Código:
####Select species and effort data
data <- read.csv(here("data", "splist_filtered_2017_04d24.csv"), sep = ",")
ef <- read.csv(here("data", "effort.txt"), sep="\t")
####Ordenando data por ordem e por FO:
data <- data[order(data$fo),]
str(data)
## 'data.frame': 47 obs. of 11 variables:
## $ sp_id : int 1032 1038 1022 1078 1079 1028 1035 1080 1081 1013 ...
## $ class : Factor w/ 1 level "Mammalia": 1 1 1 1 1 1 1 1 1 1 ...
## $ order : Factor w/ 8 levels "Artiodactyla",..: 3 3 2 8 8 2 3 8 8 2 ...
## $ family : Factor w/ 17 levels "Canidae","Caviidae",..: 5 5 11 8 8 14 5 8 8 1 ...
## $ genus : Factor w/ 36 levels "Cabassous","Canis",..: 1 27 7 4 6 26 10 31 31 30 ...
## $ species : Factor w/ 47 levels "albiventris",..: 43 23 10 36 31 15 34 20 45 44 ...
## $ species.1 : Factor w/ 47 levels "Cabassous tatouay",..: 2 36 8 5 7 35 14 41 42 40 ...
## $ iucn_status: Factor w/ 5 levels "DD","IN","LC",..: 3 5 3 5 3 3 3 3 3 4 ...
## $ sp_code1 : Factor w/ 47 levels "Caba_tato","Caba_unic",..: 2 36 8 5 7 35 14 41 42 40 ...
## $ sp_code : Factor w/ 47 levels "Caba_tato","Caba_unic",..: 2 36 8 5 7 35 14 41 42 40 ...
## $ fo : num 0.00694 0.00694 0.01389 0.01389 0.01389 ...
unique(data$sp_id)
## [1] 1032 1038 1022 1078 1079 1028 1035 1080 1081 1013 1012 1023 1011 1074 1026
## [16] 1019 1051 1014 1055 1008 1004 1037 1006 1025 1002 1031 1053 1003 1052 1021
## [31] 1017 1039 1068 1007 1020 1073 1040 1056 1015 1016 1072 1029 1009 1024 1010
## [46] 1027 1034
head(data)
## sp_id class order family genus species
## 28 1032 Mammalia Cingulata Dasypodidae Cabassous unicinctus
## 32 1038 Mammalia Cingulata Dasypodidae Priodontes maximus
## 19 1022 Mammalia Carnivora Mephitidae Conepatus chinga
## 44 1078 Mammalia Rodentia Erethizontidae Chaetomys subspinosus
## 45 1079 Mammalia Rodentia Erethizontidae Coendou prehensilis
## 25 1028 Mammalia Carnivora Procyonidae Potos flavus
## species.1 iucn_status sp_code1 sp_code fo
## 28 Cabassous unicinctus LC Caba_unic Caba_unic 0.00694
## 32 Priodontes maximus VU Prio_maxi Prio_maxi 0.00694
## 19 Conepatus chinga LC Cone_chin Cone_chin 0.01389
## 44 Chaetomys subspinosus VU Chae_subs Chae_subs 0.01389
## 45 Coendou prehensilis LC Coen_preh Coen_preh 0.01389
## 25 Potos flavus LC Poto_flav Potu_flav 0.02083
###FIGURE 01 - MAP
Generated in ArcGis by Fernando Lima
Fig. 1. Distribution of the camera trap surveys of
medium and large terrestrial mammal communities within the Atlantic
Forest extent. Gray shows the Atlantic Forest extent with remaining
forest patches in green (sensu Ribeiro et al. 2009). Blue dots show the
geographic locations of studies.
###FIGURA 02 - SUNBURST
Esta figura foi feita no Excel, utilizando a função
sunburst
Fig. 2. Taxonomic information levels of medium and large terrestrial mammal species recorded in camera trap surveys within the Atlantic Forest. Only species considered well detected by camera traps are listed. From the 83 species reported in the database, 8 are not listed because the identification is at genera level. Another 28 species are not listed because they were considered opportunistic records of species not usually detected by camera traps (primates, bats, small rodents, and small marsupials).
###FIGURA 03 - FREQUENCIA DE OCORRENCIA
RM Demanda: Casar as cores com o sunburst!
pH Eu mudei a paleta de cores. Inseri os codigos RGB
para usar igual no Excel.
fct_rev(fct_infreq(factor(data$species.1)))
## [1] Cabassous unicinctus Priodontes maximus
## [3] Conepatus chinga Chaetomys subspinosus
## [5] Coendou prehensilis Potos flavus
## [7] Dasypus septemcinctus Sphiggurus insidiosus
## [9] Sphiggurus villosus Speothos venaticus
## [11] Lycalopex gymnocercus Conepatus semistriatus
## [13] Chrysocyon brachyurus Dasyprocta leporina
## [15] Lontra longicaudis Panthera onca
## [17] Lepus europaeus Felis catus
## [19] Myrmecophaga tridactyla Tayassu pecari
## [21] Mazama nana Euphractus sexcinctus
## [23] Sus scrofa Galictis cuja
## [25] Mazama americana Cabassous tatouay
## [27] Tapirus terrestris Mazama gouazoubira
## [29] Sylvilagus brasiliensis Puma yagouaroundi
## [31] Leopardus wiedii Didelphis albiventris
## [33] Hydrochoerus hydrochaeris Pecari tajacu
## [35] Puma concolor Dasyprocta azarae
## [37] Didelphis aurita Tamandua tetradactyla
## [39] Leopardus pardalis Leopardus guttulus
## [41] Cuniculus paca Procyon cancrivorus
## [43] Canis familiaris Eira barbara
## [45] Cerdocyon thous Nasua nasua
## [47] Dasypus novemcinctus
## 47 Levels: Tayassu pecari Tapirus terrestris ... Cabassous tatouay
colnames(data)[3]<-paste("Order")
getwd()
## [1] "D:/git/atlantic-series/ATLANTIC_CAMTRAP/src"
p<- ggplot(data, aes(x=reorder(species.1, -fo) , y=fo, fill=Order))+
geom_bar(width=0.8,stat="identity", color = "black", position="stack", size =0.3) + #dimgray
#, size = 1, shape = 1
theme_bw() +
#facet_wrap(~order)+
xlab("Species") +
ylab("Frequency of occurrence")+
theme(legend.position="top")+
theme(axis.text.x = element_text(angle=45, # pH # mudei de 90 para 45
vjust=1,
hjust = 1, # pH # adicionei
family="Times", face="italic", colour="black", size=rel(0.9)))+
geom_text(aes(label=iucn_status), position=position_dodge(width=0.7), size=3, colour="black", vjust=-0.25)+
theme(plot.margin = unit(c(0.5,0.5,0.5,1),"cm"))
cores<-c("indianred1" , # pH # artiodactyla mudar para indianred #cd5c5c rgb(205,92,92)
"coral", # pH # carnivora #ff7f50 rgb(255,127,80)
"orchid" , # pH # cingulata mudar para orchid
"burlywood", # pH # didelphimorphia #deb887 rgb(222,184,135)
"khaki", # pH # lagomorpha mudar para khaki #f0e68c rgb(240,230,140)
"darkseagreen", # pH # perisodactyla mudar para darkseagreen #8fbc8f rgb(143,188,143)
"mediumaquamarine", # pH # pilosa #66cdaa rgb(102,205,170)
"dodgerblue" ) # pH # rodentia mudar para dodger blue #1e90ff rgb(30,144,255)
#png(filename= "Fig3_v19.png", res= 300, height= 16, width=26, unit="cm")
#p+ scale_fill_manual(values=cores)
#dev.off()
# pH # mesmo que acima, mas usando os codigos
cores<-c("#cd5c5c" , # pH # artiodactyla mudar para indianred #cd5c5c rgb(205,92,92)
"#ff7f50", # pH # carnivora #ff7f50 rgb(255,127,80)
"#da70d6" , # pH # cingulata mudar para orchid #da70d6 rgb(218,112,214)
"#deb887", # pH # didelphimorphia #deb887 rgb(222,184,135)
"#f0e68c", # pH # lagomorpha mudar para khaki #f0e68c rgb(240,230,140)
"#8fbc8f", # pH # perisodactyla mudar para darkseagreen #8fbc8f rgb(143,188,143)
"#66cdaa", # pH # pilosa #66cdaa rgb(102,205,170)
"#1e90ff" ) # pH # rodentia mudar para dodger blue #1e90ff rgb(30,144,255)
#png(filename= "Fig3_v20.png", res= 300, height= 16, width=26, unit="cm")
#p+ scale_fill_manual(values=cores)
#dev.off()
Fig. 3. Distribution of frequencies of occurrence of the main species evaluated in ATLANTIC-CAMTRAPS, and their status in the 2017 IUCN Red list of threatened species. LC = least concern, NT = near threatened, VU = vulnerable, EN = endangered, CR = critically endangered, DD = data deficient, and IN = invasive species (not an IUCN category).
O mapa foi feito no ArcMap
Fig. 4. Distribution of taxonomic richness and sampling effort across Atlantic Forest sites where camera traps were used for sampling of medium and large terrestrial mammal species. Opportunistic records (see the text) were removed from this analysis.